Hi, this was how it was in a much earlier version when the plugin was in its infancy and I got a large number of requests to do the UI as it is now.
The only thing I could do is provide an option between the two ways of doing this.
I cannot promise you that I can do this any time soon as it is a low priority thing compared to other tasks. As it is, the UI clearly states that the fees are subtracted from the amount so I do not believe there is any source of confusion.
Thank you for sharing your thoughts on this.